The Doctor's Descent
by notepic4
Summary: The Doctor's sanity was never something he worried much about. But the weight of the guilt inside him, and the corruption that builds within him has pushed even his considerable mind to the edge near madness. The choices he has made have now come back to haunt him as he seeks not only a path for his future but redemption for his past.
1. A few Choice Words

**The Doctor's Decent**

Prologue: A few_ Choice_ Words…

The Doctor was ecstatic, Twilight had insisted on wanting to talk to him in the TARDIS this morning, and he was more than happy to oblige. Twilight even started to make them a snack before she gave into his insistence to make their way to his bedroom. However as soon as they had entered, Twilight turned to him and said, "Well Doctor, I think it's about time we had a very important talk…"

The Doctor froze and began to look over his favorite mare skeptically. It did appear to be Twilight Sparkle, but still something did not feel quite right…

"What about Marshmallow?" He asked, trying to hide is nervous suspicion of her identity.

A swirling purple flame ran across her body as the mare turned into an onyx black unicorn stallion with a dark blue mane with a silver streak down the middle. What interested the Doctor the most however was while his left eye was a dark blood red, his right shimmered an unnervingly hypnotic bright green. He smiled with a fanged grin and began. "Greetings, as you can see, I am not your Twilight Sparkle but a well… let's just say I am an above average Changeling looking out for your best interests."

"Who are you and why have you taken the form of Miss Sparkle?"

"Ah yes where are my manners, my name is Midnight Page, and as I have said earlier, I think it is time that you and I have… a talk about your goals." The Doctor growled and replied, "My goals are my own I suggest you leave now before I _make _you leave, I don't have time for you."

Midnight glanced around dramatically before responding to the threat. "Oh yes, terribly sorry, I had no idea doing absolutely nothing would make you _so busy_."

The Doctor frowned at the sarcasm from his uninvited guest. "I will give you one more chance to leave or I will hurt you…"

"Very well then Doctor, I will get straight to the point of why I am here then." He paused before continuing with a solemn voice.

"Enough is enough Doctor; you can't sit here forever… Eventually you _must_ choose a side."

"A side, A SIDE! That is what this is about? I am tired of all this fighting, I don't care about ponies or anything else in the universe, let them fix their own problems from now on, and I am perfectly content here doing nothing…"

"Oh really? You don't seem to be, you can barely go a few hours without leaving the TARDIS on some lust driven desire to bed every young mare you meet or go on some absurd drinking frenzy."

"What I do in my spare feel time is no concern of yours and I meant I will no longer interfere with the major events of the worlds."

"Oh is that what you think? You think you can just play around with a few mares and leave the universe to rot?"

"It's worked out fairly well so far," The Doctor said with a sneer.

"I think I finally understand now…" Midnight trailed off in thought as he watched the Discorded Doctor closely.

"Understand what? That I am no longer the man you expect me to be?"

"No I understand the reasons behind you actions."

"My reasons? How can you know what my reasons are?"

"I know because we are not you different you and I…" The Doctor rolled his eyes at the statement. "Oh I doubt the legitimacy of that."

"I was once a good pony, striving to help others despite the cost to myself, and I was corrupted as well, twice in fact, once by Nightmare Moon and then again by Queen Chrysalis." Midnight paused in memory before continuing.

"And of course I wanted to get revenge on them for what they have done to me."

The Doctor rolled his eyes again, and said in mock curiosity, "Yes of course, please tell me all about your little sob story."

"Let me finish Doctor, now as I was saying I was corrupted which created a drive for me to want revenge. However a part of me wanted to forgive them, even thank them for the gifts bestowed upon me."

"Is there a point to this?" The Doctor asked impatiently as he began tapping his hoof on the ground.

"My point is this, in the midst of the two opposing ideas; I found a third option, a neutral solution if you will." He paused and with a halfhearted chuckle continued.

"Instead of merely killing them off or forgiving what they had done outright, I made them my servants, thus not harming them but still getting the revenge of constantly humiliating the two of them. It is a far more rewarding punishment I must say…"

"Well that was all very interesting; I fail to see how it applies to _me_."

"It applies to you because it is the very same thing you are doing Doctor. You could still go back to helping the universe; they have not forgotten you despite your wish for them to do so."

"And I told you that it's not going to happen."

Midnight nodded and held up a hoof.

"Or you could simply embrace the growing darkness inside you and become something even the Master would fear to meet."

"I am nothing like him, he is a monster with no restraint and-"

"It is because of the restraint from such actions that you possess as well as your unwillingness to help others that you choose the third option."

"Which is?"

"You said it yourself Doctor, nothing. You choose to hide in your box and ignore the world around you."

The Doctor began to reply but Midnight cut him off.

"And yet you know that you cannot do so forever, at least not without losing much that makes your existence worthwhile. The Master has already warned you that the seeds of destruction have been planted."

The Doctor was silent as he stared at nothing, tears starting to well in his eyes. Midnight leaned close to his ear.

"Are their lives worth your inaction, Doctor? Are you truly unfeeling to their existence?"

"I would only endanger them further were they closer to me, that was the reason they are targeted in the first place," he countered.

"Exactly Doctor, and since they are close to you, they may be harmed. Now you can either sit here all alone and let the Master have his way with them or you can rejoin those who still care about you and do something about it!"

"I-I am tired of watching them suffer…" He admitted with a sigh as he turned away.

"And you think hiding in here will avoid that, you must realize that they will face hardships because of your affiliation with them."

"And what do you expect me to do? Be the valiant hero as I slaughter whole worlds once again just to protect the ones I value more than the thousands of lives of the dead worlds?" The Doctor's coat flickered to a light tan as he shivered.

"I expect you to decide upon your path, the time for running is just about up Doctor…"

The Doctor screamed in frustration as he punched the wall of the TARDIS, tears streaming down his face as he shuddered. "I can't do this anymore, to be the patriarch of one world as I wipe others from existence…" Midnight paused and put a reassuring hoof on his shoulder.

"If you do decide to start helping ponies again, I would start by repairing your relationship with your old assistant Derpy, which should not be difficult given her feelings for you."

"Why would I need her, I have Twilight now, a powerful unicorn at my side that is intelligent, clever, and-"

"And emotionally unstable and prone to suicidal actions despite her reassurances that she can handle the new stress in her life since you have grown close to her. Do you truly think she can shrug off your actions so easily, especially the ones involving all those other mares…?"

The Doctor looked up; his eyes burned in a cold anger as he met Midnight's own judging stare.

"You can't know that, and even if that were true, she is getting better."

"Oh yes, she is getting better, and is currently being cared for in a hospital primarily equipped to assist the deranged from harming themselves or each other, do you honestly think she would be fit for any adventures in the near future?" The Doctor glared at him as his coat faded back to gray.

"And what makes Ditzy such a lovely candidate? She has her flaws as well."

"Of course she does, however Ditzy has the advantage of being used to your adventures and the stress and dangers they bring, furthermore she is more than willing to pledge herself to you whole heartedly if you would but accept her and help others again. And I believe apologizing for your abuse to her will go a long way in any case."

"And what of her foals do expect me to take them with us? Because I doubt she will leave them behind."

"Oh I think they could come along for the ride in the TARDIS, after all it's not like you are running out of room!" Midnight's voice echoed eerily within the confines of the TARDIS.

"Because if you do not, and even if you somehow convinced her to leave them, _your _foals will be harmed without further protection."

"Bah, they have-"

"One stallion, which while committed to the task of protection and skilled in his profession, is at the end of the day still only one stallion."

"Fine, I will call in a few favors and get them more-"

"And just who pray tell would you call? You have made very few allies as of late and I somehow doubt your old ones would rush to aid you in your current state."

"If I decide to let her join me again, do you really think she would make much of a difference?"

Midnight Page smiled knowingly. "Now Doctor, I would not count her out so quickly, do you even of her special talent?"

"Oh yes, her ability to destroy anything she sits on? Or is it her ability to betray the ones close to her because of some ideal for the need to help and care for others?"

The Changeling shook his head. "Think about her cutie mark Doctor."

The Doctor paused before announcing in mock realization, "Ah of course, her ability to nag you constantly with that bubbly and innocent attitude of hers!"

Midnight sighed in frustration as he resisted the urge to face-hoof and smack the Doctor.

"No Doctor, her ability is the creation of bubbles."

The Doctor burst out laughing and fell down onto the floor in hysteria.

"B-bubbles? H-how could possibly be useful to me, for a moment there I thought you were serious!"

Midnight groaned and shoved him against the wall and growled angrily as he snatched the Doctor's sonic screwdriver from his hoof.

"I'll give you a hint, it has something to do with this, and you are a smart stallion, so I assume you can figure the rest out on your own, if not…. Nightmother help us all…."

"Oi, give me back my sonic screwdriver!" The Doctor growled and reached for his beloved tool, only for Midnight to toss it behind him, falling before the silently observing Ananta, who placed a hoof over the object but made no move to return it.

"Are you really picking his side, if he gets his way I will go back to a life of danger…?"

Ananta moved to nudge the screwdriver back over to the Doctor when Midnight chimed in, "And if the Doctor gets his way, he will lose all he cares about and spend the rest of his existence moping about in here, either depressed, mad or perhaps both. Now tell me, is that a fate you wish for him?"

Ananta looked between the struggling stallions before shaking her head and fading into a gold mist back inside her hour glass, leaving the sonic screwdriver where it lay.

Midnight suddenly released his hold and chuckled a bit as the Doctor fell over with the sudden lack of resisting force.

"I will take my leave now Doctor, I cannot decide for you what your actions shall be, I only hope it will consider what I have said and choose wisely, after all your life is not the only one at stake. And do try and give Ditzy a chance should you choose to return to your old habits. She is quite a surprising mare in more ways than one…"

With that Midnight Page stepped into a shadowy dark purple portal and disappeared, leaving the Doctor to think. The Doctor slowly got up and approached his screwdriver. But he was strangely reluctant to pick it up; as if doing so would be to signify a choice he had yet to decide. He idly glanced at his bed, causing his coat to flash tan once again at the sight of his bedspread covered in bubbles. He could still remember the day he bought it in playful reference to Ditzy's cutiemark, and even now despite what had occurred between them, it comforted him with the warm memories they had shared from their time spent together. Shaking his head and cursing himself for thinking so foolishly he turned away from his bed in search of a stash of his butter, perhaps a snack would help him decide. The Doctor took a bite of a stick that had been left out from earlier and chewed thoughtfully on what his strange intruder had said. Suddenly the world span and everything faded to black…


	2. A Shadow of a Shadow

**The Doctor's Decent Chapter 1: A Shadow of a Shadow**

A strange noise echoed in the dark void of my mind. It was akin to a metallic clank of a gear combined with the telltale sound of my TARDIS traveling through time. But that could not be possible, unless Ananta decided to well drive herself but even if that were possible, where would she go? The eerie sound was suddenly silenced as I drifted closer to consciousness…

I groaned as pain coursed through my head when I tried to get up. Slowly I leaned against a nearby table for support and ran a shaking hand through my hair. Wait, I have a hand? After a moment my brain finally caught up to the rest of me and I became aware of my now human form. A shattered mirror nearby only confirmed my new appearance, but how could this even happen? I did not regenerate, or if I had, it was the least painful regeneration I have experienced yet. Walking felt very awkward for a moment as I hobbled unsteadily around the room I was in looking for clues as to where I was and how I had gotten here. It appeared to be an old manor of some sort, and it was either abandoned or in despite need of repair judging from the less than productive ceilings job of preventing the rainfall from drenching everything inside. After finding my bearings in the near pitch black room, I slowly made my way out the doorway. A gust of wind swirled around me and a piece of faded parchment collided with my face. Despite its apparent age, I could still make out the message.

_Dear Doctor,_

_You may be wondering how you came to this place and for what reason, and I assure you it is an important one. You see, though you will no doubt come to a decision as to what path you will take in due time, I am afraid that the universe does not have that time. And while yes you can manipulate much of time itself due to your Time lord heritage, circumstances have reached the point where your little respites in your TARDIS are no longer an option. And so I have taken the liberty of opening your mind to this place. While your body remains in the dimension you have left it, your mind now resides within the confines of a world founded upon the state of your sanity. Your task is to traverse these halls to the Inner Sanctum where I await you. I suppose you should know that you will be released from this world upon my death, though I hope it will not come to that. I warn you that while you have escaped the physical changes of your corruption, it is very __**real **__in this world and has taken the form of a dark shadow in the likeness of the one who corrupted you. Know that you cannot fight it here, at least not directly. As you make choices upon your morals and face a few challenges here and there, it is my hope that you will learn not only your identity but your chosen path in life as well. My finial piece of advice is this, pay close attention to the ones you trust, as they shall provide the strength that he never had. And that strength could very well be your saving grace in such a place as this._

_I await our meeting in the Inner Sanctum,_

_Midnight Page_

My hands shook from the realization that I was trapped here, in this strange world of my mind without my sonic screwdriver, without my TARDIS, I didn't even have an assistant to share this burden. But perhaps this time I shouldn't have anything to lean on, after all I am being forced to learn about who I truly am. Still the fear inside me heightened the creak of every step onto the aged wooden planks. I was not sure why, but had a strange feeling that I should head toward the source of the water. Eventually I came across a door labeled Archives. Finding no reason not to, I quickly opened the door and saw an unsettling image before me. A decaying corpse lay under piles of what seemed to be broken bottle of aged whiskey. Resisting the urge to gage, I moved on to the next room that held a lit furnace. Decaying books lay scattered around it and a part of me worried about a potential fire hazard. As I was moving the books (many of which fell apart in my grasp) a good distance away, I noticed a particular book on a small table near the furnace that was left open to a page describing various tools the writer deemed necessary for survival any ware. The section focused primarily on the usefulness of tinderboxes to light the way while exploring unknown locations. Figuring it was sound advice I helped myself to the small bundle of tinderboxes near the dead man's side. Finding nothing else of interest, I decided to explore the next room. Within that room a candle was lit upon an old desk. What caught my eye however was the lantern that rested upon the edge of the desk. A note beside the afore mentioned lantern read, "_Your guiding light though darkest of times. Never waste its precious gift as it is the key to preserving not only your sanity in this world, but your heart as well. Think of the oil it requires as the emotions and morals within your heart. Should the darkness inside you spread beyond and corrupt what remains of your inner light, you will become nothing more than the shadow of the shadow that hunts you even now."_

Despite the cryptic notes warning, I immediately poured the abnormally bubbly oil into the lantern to check its functionality. With the golden glow of the lantern's light brought clarity to the shifting room and I noticed an off lever on the far side of the adjacent wall to my left. After a brief struggle, I managed to pull it down and a concealed door slowly opened near me. I quickly snuffed out my lantern and entered the new room. But as soon as I passed the threshold of the doorway, the scream of young woman made me jump back in reflex. Before I could investigate the source of the scream however, a crushing void defeated my willpower and everything faded to black…

(Authors Note: A few things you should know before you go any further is a few events I have changed due to both my personal preferences as well as for the story itself. For now the most important one is that after Twilight's suicide attempt, she was transported to an asylum (this will be explained later) that is secretly run by the Master. And so obviously the Doctor never came by to comfort her, though he is not aware of her current location, he only knows she is at a location in which she is being cared for. He chooses not to go and comfort her out of guilt of being a cause of her suicide attempt in the first place. Most of everything else that has happened in the cannon Doctor Whooves storyline has happened and I will try to mention any important changes I have made as the Doctor progresses.)


	3. Poof

**The Doctor's Decent: Chapter 2: A Muffin a Day keeps the poof away **

I groaned as consciousness slowly retuned to me. The first thing I realized is that somehow I had left the strange world he had been imprisoned in and had awoken in a forest, and it was the Everfree if my suspicion was correct. My body ached from lying on the cold damp ground for what seems to have been most of the day. The sun had just begun to set overhead the tall trees that had suddenly become much more ominous. And to top it off, a storm looked to be fast approaching. With a sigh I got up and started toward where I believed my TARDIS was located. A rustling in the bushes made my hearts start to beat faster as I recalled the creatures I had faced before in this forest, and this time I lack both my sonic and an assistant. Gathering my wits and berating myself over what I dearly hoped was simply a squirrel, I boldly exclaimed, "W-who's there?"

A familiar gray pegasus poked her head out of the brush and meekly answered, "Hello Doctor… it's good to see you again."

I scowled and considered leaving my _former_ assistant then, but somehow curiosity got the better of me.

"What are you doing out her in the forest? Are you following me or…"

I examined her closely and noticed a particular key hanging around her neck. "Were you the one that got me here in the first place? I fainted in my TARDIS, and I don't think I just "sleep walked" all the way out here…"

Derpy looked down at her saddlebag embroidered with the post office insignia and answered. "I have recently became Ponyville's local mailmare and I-"

"_You _a mailmare? Please your directional skills are horrendous, they must be desperate to higher you. A newborn foal could do a better job."

"I-I usually only do the homes around my local block so I don't err… so I am less likely to get lost when I deliver but nopony else is willing to deliver mail to Zecora so I volunteered."

"That still does not explain what you are doing in that bush conveniently so close to where I woke up, enjoying me suffer are you?"

"N-no Doctor I would never do that, my bag ripped during my flight and a bunch of letters fell out and landed in this bush. Meeting you was a complete coincidence honest…"

Sighing I noticed the large hole in the mare's bag, perhaps what she said was true.

My train of thought was interrupted as my stomach growled loudly in complaint for the lack of food. Not surprising after wondering inside that decaying house for hours. Derpy looked away again and murmured in a hesitant voice, "If… if you are hungry I can make you some muffins back home, English muffins with butter, just like old times."

While normally I would refuse her offer, fatigue and hunger overpowered pride in this case as I have no idea where my TADIS is and was close to staving.

"Very well, let's go back then, at least this will allow me to show you how I have become a better pegasus than you will ever be in any case."

_Hey Doctor, maybe while you're at it making Derpy your willing servant/slave, you should look into getting her a uniform. I know if a few places that sells the perfect maid outfits and…_

Derpy's POV

I frowned as we flew off toward the setting sun. I could not help but admire the Doctor as he flew and gradually glided closer to him. Suddenly his wings stood ridged and began to descend at a rapid pace.

"D-Doctor what's wrong?" I screamed as I rushed to catch him.

Doctor's POV

"I-I don't know, my wings are stuck!" I exclaimed, a slight blush deepening across my face. Fortunately Derpy caught me just before I would have hit the ground. Unfortunately this caused a rather grumpy manticore to awaken from his nap and growl at us threateningly.

"I don't think I can carry you away fast enough Doctor…" We could not get away in my state, and while I doubted she would abandon me to get away from the best, I could not blame her if she did so after my… less than gentle treatment of her.

"We need to get out of here, stupid wings why now? I knew those voices would be the death of me…"

Derpy POV

I ignored his rant (something everypony who met him learned to do at some point) and started running my hoof alongside his wings and back, causing him to shiver as he spoke, "W-what do you think you are doing? This is not the time for some desperate near death se-ahh!" The Doctor yelped as I found what I had been looking for and bit down onto a section of his back.

"What was that for? Are you trying to get me killed you stupid-" He suddenly noticed the lack in tension in his wings and found that he could flap them again, if stiffly.

"How did you-"

"There's no time for that now Doctor, we need to go!"

"R-right but I want some answers…"

Doctor POV

After dodging the sweeping claw of the manticore and flying up to the safety of a nearby cloud, I turned to Derpy and glared expectantly for her to explain her actions.

"I bit a small clump of nerves in your back responsible for the blood flow to your wings. When I cut it off, the stiffness in your wings decreased enough to allow you to flap them for a short time…"

I nodded but asked, "Isn't biting that area dangerous?"

Derpy looked away and nodded. "B-but I have done it several times before and it was an emergency, I'm sorry..."

_Never expected her to be a biter eh Doc? Maybe she learned it from Dash…_

'Shut up this is not the time for that, you are the reason I was in that situation in the first place!' I argued, feeling my wings start to stiffen once again.

"Where did you learn about that?"

"Well in flight school I was um… not the best of flyers and so I usually was grouped with some ponies that had their own particular needs or problems with flying. One of them was a mare named Dust Feather who had spontaneous wing stiffening whenever she flew for too long or while really stressed. She told me about the clump of veins and how they could be used as a temporary fix for her to reach the ground safely. The spot is in a bit different place on stallions than mares so it took me a moment to find it…"

Curiously I moved around her and examined her back closely. Realizing my intent, Derpy obliged and lifted her wings up. After a moment, a slight knot formed between her shoulder blades that was centered between her wings. I leaned to inspect it further as Derpy continued her lecture on Pegasus anatomy.

"The knot is much more prominent if your wings are-"

She froze as a bit down on the knot, causing her wings to stand rigidly for a moment before they began to start twitching.

"D-Doctor don't do that!"

I chuckled at her sudden embarrassment and watched as she tried to reposition herself awkwardly on the cloud. After a moment of floundering she eventually got back up and met my gaze blushing heavily.

"Doctor you really shouldn't do that…"

"And why not?"

"B-because unless it's an emergency, biting there is usually considered a very intimate action. It's like proving complete dominance to the pony you are biting, akin to biting their neck…"

Memories flashed to Rainbow Dash's treatment of me, suddenly all that biting around my body made a lot more since. I shuddered as any relaxation that my wings had gained disappeared.

"We should probably head back to my home soon, it's getting dark." Derpy observed after my wings had finally calmed down again. I nodded and we reached her house without further incident. Just as I entered the room, it began to stretch and spin. I groaned in pain as the dizziness caused me to fall forward, thankfully onto a carpeted floor.

"So would you like a few buttered English muffins or…?"

She trailed off as she notice me collapsed on the ground behind her.

"Doctor! What is happening to you? Do you want me to get help or-"

"N-no help…nothing they can…do for me"

Tears began to stream down her face as she whispered my name over and over.

"I-I am…not regenerating you…idiot! I am…" Before I could finish the black void swallowed my existence and I waited to wake up in that living nightmare once again…


End file.
